The emitting light in fireflies or other bioluminescent species arises from the electronic relaxation of oxyluciferin, an organic compound resulting from the oxidation of the D-luciferin substrate inside an enzyme called luciferase. These systems are already used in applications such as cell cancer detection. One of the challenges of the modelling of such systems is to reproduce the experimental absorption, fluorescence and emission spectra measured inside the protein or in a solvent. The models give insights for a better understanding of the experimental results and for further design of new bioluminescent systems. Here will be presented the methodologies and modelling tools that are used to study the spectroscopic proprieties of bioluminescent systems. There is a need of quantum mechanics, molecular dynamics and hybrid (QM/MM) methods.[1] The experimental emission and absorption spectra are accurately reproduced when the dynamic of the system is taking into account. Information of the nature of the transitions can be taken from the modelling and insights of the influence of the protein environment can be highlighted. Challenges and perspectives of the modelling for bioluminescent systems will be highlighted with examples.